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RNA Sequence Assembly

RNA Sequence Assembly. WEI Xueliang. Overview. Sequence Assembly Current Method My Method RNA Assembly To Do. Sequence Assembly. Goal : get the DNA/RNA sequence. Machine cannot read whole genomes in one go, but rather small pieces between 20 and 1000 bases. Define: Read = Tag = Fragment.

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RNA Sequence Assembly

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  1. RNA Sequence Assembly WEI Xueliang

  2. Overview • Sequence Assembly • Current Method • My Method • RNA Assembly • To Do

  3. Sequence Assembly • Goal : get the DNA/RNA sequence. • Machine cannot read whole genomes in one go, but rather small pieces between 20 and 1000 bases. • Define: Read = Tag = Fragment

  4. De novo sequence assembly

  5. Overview • Sequence Assembly • Current Method • My Method • RNA Assembly • To Do

  6. De novo sequence assembly • Calculating the overlap need huge amount of time.

  7. DE BRUIJN GRAPH • K-Mer : Length k substring of the Tag. • Each nodes only have 4 out degrees at most. • Hashing the node. • “CTG”=>(132)4=(30)10 • “CTG”=>”TGG” • (132=)4 shift left. • (1320)4 module (1000)4 • (320)4 + (3)4 ‘G’ • (323)4

  8. DE BRUIJN GRAPH (CONT’) • If there are repeats, like ”GACT” • 3-Mer De Bruijn can not know which way is the correct way. 6-Mer can get the correct sequence. • Larger K, better result.

  9. De novo sequence assembly • Suppose use K = Length of Tag. (20-Mer) • TGACGTAGCTATGTATTTTG • GACGTAGCTATGTATTTTGT (no 20-Mer) • Coverage is not enough to support large K.

  10. Overview • Sequence Assembly • Current Method • My Method • RNA Assembly • To Do

  11. MY METHOD. • Tag length=6, K=3 • When we have • AAGACT? • Try all the way: • AAGACTC • AAGACTT • AAGACTG • Check Tag : • AGACTC • The correct way should be AAGACTC

  12. Overview • Sequence Assembly • Current Method • My Method • RNA Assembly • To Do

  13. RNA ASSEMBLY

  14. ALTERNATIVE SPLICING • The graph • All cDNA sequences.

  15. RNA ASSEMBLY’S PROBLEM • Merge? • Index the sequence.

  16. RNA ASSEMBLY’S PROBLEM(CONT’) • Solution?

  17. RNA ASSEMBLY’S PROBLEM(CONT’) • Index Tags

  18. RNA ASSEMBLY’S PROBLEM(CONT’) • Solution? • Speed?

  19. SINGLE TAG’S LIMITATION • |Yellow Sequence| >= Length of Tag • Length of Tag 25-100bp. • Single Tag is not enough!

  20. DATASET - PAIRED END TAGS • Fragment length usually > 1k • Some RNA sequence is shorter than 1k.

  21. TO DO • Handle large data-sets. (10G) • Improve accuracy. • Using PETs data.

  22. Thanks!!

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